Herd immunity

Since the 8th of March, There Have Been 9,484 *Fewer* Deaths Than Normal

Today the ONS announced that there were 8,808 deaths in England and Wales in the week ending 2nd July 2021. This is 118 more than the previous week, but still 5.2% below the five-year average. Here’s the chart from the ONS:

Deaths in England and Wales have now been below the five-year average for 14 of the past 17 weeks. Over that time, there were 9,484 fewer deaths than you’d expect based on the average of the last five years. And recall that, due to population ageing, the five-year average understates the expected number of deaths. Hence the true level of “negative excess mortality” is even greater.

The number of deaths registered in the week ending July 2nd was below the five-year average in seven out of nine English regions. (Only the North East and North West saw positive excess deaths.) Compared to the five-year average, weekly deaths were 10.7% lower in the East of England, and a remarkable 12.1% lower in the South East.

The fact that “negative excess mortality” has now persisted for three consecutive months supports the hypothesis that deaths were “brought forward” by the pandemic.

It’s been widely noted that the link between cases and deaths has weakened substantially in recent weeks, thanks to the build up of population immunity. Although the number of daily infections has surpassed 20,000, the number of daily deaths remains in the low double digits. However, the situation is actually even more positive: measured by excess deaths, the pandemic hasn’t taken any lives since early March.

The Outbreak Point: Are Covid Outbreaks Triggered When the Viral Load in the Air Hits a Certain Threshold?

In recent posts I’ve been exploring the question of why COVID-19 (much like other seasonal viruses) has a Jekyll and Hyde-like nature, being puny for much of the year then exploding in short, sharp outbreaks for a few weeks at a time, usually though not exclusively in the winter. I argued in a post last week that seasonality appears to be driven largely by cycles in the human immune system (though there may be environmental factors such as UV radiation, temperature and humidity as well). The trigger for the somewhat irregular (and not necessarily winter) outbreaks appears to be the appearance of a new variant (or virus) that is able to infect slightly more people, amounting to just one in 18 additional people when estimated from the secondary attack rate. The end of the outbreaks then corresponds to the exhaustion of the small pool of newly susceptible people and the restoration of the temporarily disturbed herd immunity.

I noted that the difference between a surge and a decline amounted only to a small absolute change in the R growth rate, from 1.3 during a surge to 0.8 during a decline, and that the shift between these rates often occurs very abruptly. This means that infected people quite suddenly start infecting 1.3 other people before, around three and a half weeks later, just as suddenly switching back to infecting just 0.8 people. This change in R is reflected in a similar change in the secondary attack rate (the proportion of contacts an infected person infects), which varies between around 15% during surges to around 10% outside of them. I observed that this difference is small enough to be explained by a slightly increased susceptibility to a new variant and a subsequent restoration of herd immunity a short time later.

After writing this it occurred to me that with such a subtle trigger it would seem that outbreaks should be highly sensitive to the amount of social contact people have with one another, and thus to the imposing and lifting of restrictions (or to voluntary social distancing). Indeed, it is logic like this which presumably explains why SAGE members and other scientists persist in believing in the efficacy of lockdowns regardless of how much data emerges showing they don’t make any significant impact on the infection or death rate.

A recent set of SAGE minutes explains the logic of restrictions:

Professor Tim Spector Calls for Vaccination of Children ‘Because Delta Variant’

King’s College London Professor of Genetics Tim Spector dismayed many of his Twitter followers yesterday by calling for the vaccination of older children. The reason? Because the Delta (Indian) variant means we now need 85% of the population vaccinated to reach herd immunity, he claims.

Professor Spector, who leads the ZOE Covid symptom study, was replying on Twitter to Israeli scientist Eran Segal, who tweeted: “Before Delta, Israel reached herd immunity or close to it. To regain herd immunity, we need to vaccinate as many of the 1.2 million over the age of 12 who have not yet been vaccinated.”

Spector wrote: “In the U.K. with delta we need to get near 85% of the population – which also means vaccinating older children.”

In calling for this, Prof Spector appears not to be concerned about the worries of many scientists including members of the JCVI about the benefit-versus-risk balance for teenagers in having the vaccine, or the ethics of suggesting children should be given a vaccine with no long-term safety data not for their own benefit but for the benefit of others.

The notion that a threshold of herd immunity will only be reached if 85% of the population is vaccinated also bears no relationship to real-world data. It’s not entirely clear what Segal and Spector mean by herd immunity in these tweets, but if they mean that without an 85% vaccination rate the Delta variant will continue indefinitely to cause mass hospitalisations and deaths, then perhaps they would like to explain why India’s test positivity rate entered a sustained plummet nearly two months ago, despite the Delta variant being dominant and the country at that point having only 2.5% of its population fully vaccinated? (The figure now stands scarcely higher at 4.3%.)

Does This Explain Why COVID-19 is Normally so Puny But Occasionally Goes Bang?

I wanted to come back to the question of what causes COVID-19 occasionally to have explosive outbreaks. We’ve had two in England so far. Using the graph below (produced by Imperial’s REACT study using symptom-onset reports from their antibody survey, so no PCR tests involved) we can see when they occurred. The first occurred from around February 25th to March 19th 2020, ending after about three and a half weeks, as abruptly as it began. The second got going around December 2nd, and ended – once again abruptly after three and a half weeks – on December 25th. As the lines below indicate, these starts and stops bear no relation to when lockdowns were imposed or lifted (the red and blue lines respectively).

Given that (as we can see) Covid was around in England throughout the winter of 2019-20 (arriving in November according to this graph) and was also simmering away in the autumn of 2020 without taking off, a key question is what triggers the beginning and end of the more explosive outbreaks?

Another way of putting the same question is: why does COVID-19 occasionally, Jekyll and Hyde-like, transform from a relatively gentle, not very infectious disease into a super-infectious disease for a few weeks, before suddenly returning once more to its largely benign form?

Perhaps surprisingly, Covid in England has only been in ‘Hyde’ form for about seven weeks in total so far, with the R rate (the speed at which the epidemic is growing) only going significantly above one (indicating an exponentially growing epidemic) for around three and a half weeks in February/March 2020 and three and a half weeks in December 2020. The rest of the time it’s been up and down in different regions, particularly in the autumn, but there’s been no nationwide surge. What, then, on those two occasions triggered the disease to become briefly so much more infectious across the country?

“The NHS is Going to be Smashed in Weeks”, Cummings’s Data Geek Told Boris – on the Day Infections Peaked in London

Lockdown Sceptics‘ readers have had their fill of Dominic Cummings stories in the last 24 hours. However, his claim, repeated yesterday in front of MPs, that without a lockdown last March “the NHS is going to be smashed in weeks” cannot go unanswered.

These are the words that, according to Cummings, data analyst Ben Warner said to Boris Johnson when he confronted him with “evidence” on Friday March 13th 2020 that a lockdown was necessary to prevent the NHS being imminently overwhelmed.

March 12th and 13th 2020 are notable for being the days when various Government advisers did the media rounds to sell to the public the idea of “building up some kind of herd immunity“, as Chief Scientific Adviser Sir Patrick Vallance put it on Radio 4’s Today programme. Prior to this, the Government had been sticking to the script of their action plan and pandemic preparedness strategy that did not talk about herd immunity (even if it implied it) but about mitigation of the impact of the disease.

Whose idea it was to start talking about building up herd immunity by infection is not clear, and, despite pontificating for seven hours yesterday, Dominic Cummings did not enlighten us on that point. The move was, however, disastrous for Government public relations, as the concept jarred with the public. Worse, it was criticised by scientists and health care professionals, who argued that herd immunity through infection was not a sound policy aim even if it would be the inevitable result of the mitigation strategy. Dr Adam Kucharski from the London School of Hygiene and Tropical Medicine put the matter succinctly on Twitter:

Why Ministers are Telling the Truth When they Say ‘Herd Immunity’ Was Never Government Policy

Home Secretary Priti Patel appeared on Andrew Marr on Sunday and repeated the Government line that “herd immunity” was never the Government’s strategy. “Our strategy was always about protecting public health, saving lives, and protecting the NHS,” she said.

Outside Government it seems to be accepted, including by its defenders, that this is untrue and herd immunity was originally part of the Government’s plan. Referring to allegations by Boris Johnson’s former Chief Adviser Dominic Cummings that the Government was following a herd immunity strategy until March, UnHerd editor Freddie Sayers writes:

Cummings’s big accusation that the initial pandemic response plan, based on flu, included the goal of herd immunity is long-established, as is the fact that the Government initially considered it, then deviated from it rapidly when its implications became clear.

If this is so, why does the Government continue to deny it?

Anne-Marie Trevelyan, the Minister for Business, appeared on Good Morning Britain today to try to explain:

It was never the policy of this Government. Boris Johnson was very clear that the only thing that mattered was that we make sure that we saved lives and we keep our NHS safe and able to function, not only to protect those who might get Covid but also everybody else. … I’m very comfortable that the Prime Minister never had as his policy herd immunity.

Trevelyan was asked about remarks by Chief Scientific Adviser Sir Patrick Vallance on March 13th 2020, when he said: “Our aim is to try and reduce the peak, broaden the peak, not suppress it completely. Also, because the vast majority of people get a mild illness, to build up some kind of herd immunity so more people are immune to this disease.”

The Times explains the distinction Trevelyan and the Government are seeking to draw.

Cummings Claims That Government’s Original Plan Was ‘Herd Immunity by September’

In early March of 2020, there was rising public concern that the UK was taking an altogether different approach to its neighbours, leading some people to joke that Britain was the world’s “control group”. To allay public fears, the health Secretary Matt Hancock wrote an op-ed in The Telegraph on March 15th claiming that “herd immunity” was not part of the government’s plan. Here’s the full quote:

We have a plan, based on the expertise of world-leading scientists. Herd immunity is not a part of it. That is a scientific concept, not a goal or a strategy. Our goal is to protect life from this virus, our strategy is to protect the most vulnerable and protect the NHS through contain, delay, research and mitigate.

Now Dominic Cummings – the former chief advisor to Boris Johnson, who left No. 10 “with immediate effect” in mid November – has claimed that the government did intend to pursue a “herd immunity” strategy. At 3:38 this afternoon, Cummings tweeted:

Media generally abysmal on covid but even I’ve been surprised by 1 thing: how many hacks have parroted Hancock’s line that ‘herd immunity wasn’t the plan’ when ‘herd immunity by Sep’ was *literally the official plan in all docs/graphs/meetings* until it was ditched

In a subsequent tweet, Cummings elaborated on why the government’s original plan was “ditched”. He writes:

In week of 9/3, No10 was made aware by various people that the official plan wd lead to catastrophe. It was then replaced by Plan B. But how ‘herd immunity by Sep’ cd have been the plan until that week is a fundamental issue in the whole disaster

What Cummings says is of course broadly consistent with the statements Chris Whitty and Patrick Vallance had made up until the date of Hancock’s article, as well as with the infamous ‘UK Influenza Pandemic Preparedness Strategy 2011’. In a hearing of the Health and Social Care Committee on March 5th, Whitty said, “what we’re very keen to do is not intervene until the point we absolutely have to, so as to minimise economic and social disruption.”

Opinions obviously differ about whether the original plan would “lead to catastrophe”, but it’s interesting to have an insider’s perspective on the Government’s early planning.

Stop Press: In a further tweet, Cummings has accused the Government of lying. He writes:

No10 decided to lie: ‘herd immunity has never been… part of our coronavirus strategy’. V foolish, & appalling ethics, to lie about it. The right line wd have been what PM knows is true: our original plan was wrong & we changed when we realised

The Data Suggest We Achieved Herd Immunity Before the Vaccines Were Rolled Out

We’re publishing an original piece of data analysis today by a leading British scientist – a full professor at a major university – who wishes to remain anonymous. He believes the data show that the population of Britain had surpassed the herd immunity threshold in December, before the vaccines were rolled out. He’s not an anti-vaxxer, and thinks it was right to immunise the elderly and the vulnerable, but doesn’t believe we should vaccinate the rest of the population. Here is a summary of his analysis:

  • Population immunity played a major role in ending each wave of SARS-CoV-2 infection
  • Herd immunity thresholds differ by about two-fold across England, and have been reached
  • Different herd immunity thresholds correlate with regional differences in ethnicity and air temperature – possibly both operating by changing the rate of indoor contacts
  • The Infection Fatality Rate has changed dramatically during the pandemic: it first rose during (and possibly because of) lockdowns, and then fell by over eight-fold as older and vulnerable individuals were vaccinated. It is now so low, and herd immunity so well established, that vaccinating younger adults and children with novel genetic technology vaccines cannot be medically or ethically justified.

This piece is very much worth reading in full.

Britain Will Achieve Herd Immunity on Monday

According to a Telegraph exclusive, the number of people with protection either through vaccination or previous infection will hit 73.4% on April 12th – the herd immunity threshold. Sarah Knapton, the Telegraph’s Science Editor, has more.

Britain will pass the threshold for herd immunity on Monday, according to dynamic modelling by University College London (UCL), placing more pressure on the Government to move faster in releasing restrictions.

According to the UCL results, published this week, the number of people who have protection against the virus either through vaccination or previous infection will hit 73.4% on April 12th – enough to tip the country into herd immunity.

The number is in stark contrast to the modelling released by Imperial College this week, which suggested there was just 34% protection by the end of March.

Last week, antibody testing by the Office for National Statistics (ONS) suggested that, in the week ending March 14th, around 54% of people in England already had antibodies to the virus, and slightly less in the devolved nations.

Since then, a further 7.1 million people have received a first dose of vaccine and nearly 100,000 have tested positive for the virus, with many more acquiring a silent, asymptomatic infection.

It is thought about one in 10 people also have some innate immunity through infections with other coronaviruses – pushing population-level protection up further – while others may be immune through T-cells, which would not be picked up in antibody testing.

Worth reading in full.

Stop Press: At the end of this story there is a very encouraging note about the Government’s unhappiness with the models SPI-M is relying on for the latest advice it’s feeding the Government via SAGE. Interestingly, almost all the points the Government has raised are points raised by Glen Bishop and others on Lockdown Sceptics.

The Telegraph understands that the Government is unhappy with the pessimistic tone set by models produced by SPI-M, released earlier this week, and has asked other groups to critique the work. The SPI-M summary, presented to SAGE, suggested the roadmap out of lockdown was “highly likely” to lead to increased hospital cases and deaths this summer.

The models were criticised for using out of date and flawed assumptions about levels of population immunity and effectiveness of the vaccine as well as failing to factor in reductions in transmission due to vaccination and seasonality.

Prof Carl Heneghan, director of the Centre for Evidence Based Medicine at Oxford University, said: “In my 20-plus years as a doctor, I’ve never come across a summer surge in a respiratory infection in the UK. The modelling now keeps changing dramatically, so it’s hard to see how it helps us. What we really want to do is look at the real-world data and make decisions from there.

“One of the problems is nobody is going back and checking whether the modelling matched up with the reality. We know that modelling in schools has not helped us because it was incorrect. So we need to have a reality check.”

Stop Press 2: Matt Hancock has dismissed claims that herd immunity will be reached next week. The Times has the story.

[The Health Secretary] appeared unmoved by the optimistic claims. “I was told by some scientists that we were going to have herd immunity in May and then in June and then after that,” he told LBC.

“What I prefer to do is watch the data. We’ve set out the roadmap, the roadmap is really clear. It is our route back to normal. We’re on track to meet the roadmap and that is our goal.”

Pressed on why he was not accepting UCL’s claims, Hancock replied: “I think we have taken the right course in plotting our way to freedom and doing it carefully because we want it to be irreversible. We have seen what happens when this virus gets going and we are seeing it getting going right now on the continent and other parts of the world – some of the scenes are really appalling.

“We want to get out of this safely and irreversibly and that’s why we set out the roadmap.”

Also worth reading in full.

New Study: Exposure to COVID-19 Confers Immunity Even When Not Infected

The mainstream preoccupation with antibodies as a signal of protection from COVID-19, coupled with worries about their declining levels, often fails to acknowledge the crucial role played by T-cells in conferring longer lasting immunity.

A new study in Nature shows that not only do people infected with SARS-CoV-2 develop lasting T-cell immunity, but so too do their close contacts who never experience a detectable infection and have no detectable antibodies.

The authors write:

Close contacts, who are SARS-CoV-2-exposed, are often both NAT [PCR] negative and antibody negative, indicating that SARS-CoV-2 failed to establish a successful infection within these individuals, presumably due to their exposure to limited numbers of viral particles or a short time of exposure. However, our analysis of the samples from 69 of these close contacts showed the presence of SARS-CoV-2 specific memory T-cell immunity.

For those infected, the study found the level of T-cell immunity was similar regardless of whether the infection was severe, moderate or asymptomatic. It also found T-cell levels stabilised and did not diminish over the course of three months, implying lasting protection.

For close contacts who were not infected, there were some differences in the quality of their T-cell immunity compared to those infected. The authors write:

The size and quality of the memory T-cell pool of COVID-19 patients are larger and better than those of close contacts. … The results show that 57.97% and 14.49% of close contacts contained virus-specific memory CD4+ and CD8+ T-cells, respectively.

Disappointingly, the study found that in those never exposed to SARS-CoV-2 (because the samples came from before September 2019) there was no evidence of T-cell cross-immunity from other coronaviruses.

In order to investigate whether the observed expanded T-cells may have originated from pre-existing cross-reactive T-cells specific for common cold coronaviruses from previous infections, we tested blood samples of 63 healthy donors collected before September of 2019. Following a 10-day in vitro peptide expansion only 3.17% of the healthy donors contained detectable levels of virus-specific memory CD4+ and CD8+ T-cells, respectively, suggesting that cross-reactive T-cells derived from exposure to other human coronaviruses do exist but are at a significantly lower frequency than those observed in close contacts.

They acknowledged that this was contrary to other recent studies and suggested the issue needed further study.

In agreement with recent reports,17,25 our data also demonstrated the presence of cross-reactive memory CD4+ and CD8+ T-cells, which target various surface proteins of SARS-CoV-2, in unexposed healthy donors. However, the failure of these cross-reactive memory CD4+ and CD8+ to expand in vitro suggests they have limited potential to function as part of a protective immune response against SARS-CoV-2. It is noteworthy that the SARS-CoV-2-reactive T-cells detected in the unexposed healthy donors in our study were lower than those detected by Grifoni et al.17 and Braun et al.26, but were consistent with those reported by Peng et al.27 and Zhou et al.28 Assumably, due to the use of different methodologies in assessing SARS-CoV-2-specific T-cell responses, it is difficult to directly reconcile the cell-number data between different studies. Thus, a thorough investigation is needed to determine whether the cross-reactive T memory can provide any protective immunity and exert an influence on the outcomes of COVID-19 disease.

The fact that exposure to SARS-CoV-2 can result in the development of more robust immunity (perhaps because of an immune system part-primed from earlier viral infections), rather than infection, is a salutary reminder of how the circulation of viruses helps us to develop and maintain healthy immune systems capable of fighting off a variety of diseases. Trying to avoid infection by staying away from people, insofar as that is possible, can be counterproductive as it can weaken our immune system by leaving us unexposed to a whole variety of pathogens.

It’s also a reminder that antibody testing is a very limited way of determining who has been exposed to and developed immunity to COVID-19. If millions of people exposed to the virus are developing immunity without ever being infected or developing antibodies, what does that mean for reaching herd immunity? It must be closer than we think.